The history of wars, not only American ones, is littered with examples of able generals falling out with their commanders-in-chief. Harry Truman did the world a service in sacking Douglas MacArthur before the general, in true Dr Strangelove mode, could finish the Korean war by dropping nuclear bombs on China. The closer parallel to what took place last night in Washington was Lyndon B Johnson and General William Westmoreland who persisted, after the Tet Offensive, in believing all those "positive indicators" that they were winning in Vietnam. Like Stanley McChrystal, Westmoreland argued that they could not win unless they expanded the war (into Cambodia and Laos). We all know what happened.

But that was then and this is now. The fact that alpha males have clashed before is of no use to the current commander-in-chief in Washington. Like it or not, the Afghan conflict is now his. It has long since stopped being a hospital pass from his predecessor George Bush. Mr Obama made it his war by following the advice, or succumbing to the pressure (whichever you believe), of the general whom he last night sacked. As McChrystal made brutally clear in the Rolling Stone profile, the general fought his corner for more troops last year with the same ruthlessness and disdain for his enemy (in this case Obama's entire national security team) which the special-ops general used to decapitate al-Qaida in Baghdad. He leaked his own policy review, which said that if he did not get more troops they would face mission failure. The White House was furious but the tactic worked. McChrystal had his way. But the surge and the counterinsurgency methods the general championed have yet to have their way. Nothing permanent is being built in the areas they are clearing and holding. Rather the reverse: the increased military presence in Marjah is fanning the flames of war in central Helmand. As the general himself said just a few weeks ago, Marjah – which was intended to be a showcase of new tactics – has become an object lesson in what to avoid. And this before the major offensive in Kandahar even takes place. The stakes for Mr Obama could not be higher.

The general could not have continued in his job after rubbishing, or allowing his senior advisers in his presence to rubbish, practically everyone he was supposed to be working with – the president, the vice-president, the national security adviser, the White House's top civilian adviser on Afghanistan, the US ambassador in Kabul. It's quite a list of players to insult. The only two to emerge unscathed from the general's tour d'horizon with the Rolling Stone reporter was the US secretary of state, Hillary Clinton, and Hamid Karzai. The Afghan president called for his retention, calling him the best commander of the war. But when the task ahead is as much political and civilian as it is military, Mr Obama could not have tolerated this feuding. In sacking a talented but maverick soldier, the president attempted to re-establish his own authority as commander-in-chief over querulous generals. With containment caps popping off gushing wells in the Gulf of Mexico, and the lingering impression created by his handling of the BP spill, that he was too detached to be a good leader, Mr Obama had no choice but to stamp his authority over McChrystal. It was important for him to say he would not tolerate division.

Mr Obama portrayed this as a change of personnel, not policy, and in passing this chalice to Gen David Petraeus as McChrystal's successor, there will be none. The real issue, however, is not a dysfunctional team, but a dysfunctional war. Dissenters are heading for the exit door. After the departure of Britain's special envoy Sir Sherard Cowper-Coles, Hanif Atmar, the Afghan interior minister, and the spy chief, Amrullah Saleh, there are perhaps worse punishments than being deprived of the command of an unwinnable war.

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